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- PDB-6ppx: Crystal structure of metal-free NeuB, an N-acetylneuraminate synt... -

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Basic information

Entry
Database: PDB / ID: 6ppx
TitleCrystal structure of metal-free NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis in complex with malate
ComponentsN-acetylneuraminate synthase
KeywordsBIOSYNTHETIC PROTEIN / TRANSFERASE / NeuB / sialic acid synthase / N-acetylneuraminate synthase
Function / homology
Function and homology information


N-acetylneuraminate synthase / N-acetylneuraminate synthase activity / N-acylneuraminate-9-phosphate synthase activity / : / carbohydrate biosynthetic process / metal ion binding
Similarity search - Function
N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. ...N-acetylneuraminic acid synthase, N-terminal / : / NeuB family / SAF domain / SAF / SAF domain / Type Iii Antifreeze Protein Isoform Hplc 12 / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal / Antifreeze protein-like domain profile. / Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain superfamily / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
D-MALATE / N-acetylneuraminate synthase
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup B (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRosanally, A.Z. / Junop, M.S. / Berti, P.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-64422 Canada
Canadian Institutes of Health Research (CIHR)MOP-89903 Canada
CitationJournal: Biochemistry / Year: 2019
Title: NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB.
Authors: Popovic, V. / Morrison, E. / Rosanally, A.Z. / Balachandran, N. / Senson, A.W. / Szabla, R. / Junop, M.S. / Berti, P.J.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
SupersessionOct 9, 2019ID: 3CM4
Revision 1.1Oct 9, 2019Group: Advisory / Data collection / Category: pdbx_database_PDB_obs_spr
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5302
Polymers38,3961
Non-polymers1341
Water6,107339
1
A: N-acetylneuraminate synthase
hetero molecules

A: N-acetylneuraminate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0604
Polymers76,7912
Non-polymers2682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8000 Å2
ΔGint-33 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.070, 76.200, 77.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein N-acetylneuraminate synthase / SynC protein


Mass: 38395.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup B (bacteria)
Gene: synC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H2VFG5, N-acetylneuraminate synthase
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 3% (v/v) MPD 1.75M Malic acid 10mM magnesium chloride 10mM N-acetylneuraminic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 29, 2008
RadiationMonochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→77.62 Å / Num. obs: 29645 / % possible obs: 98.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.035 / Rrim(I) all: 0.104 / Net I/σ(I): 2.53
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2676 / CC1/2: 0.915 / Rpim(I) all: 0.248

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XUZ

1xuz


Resolution: 1.85→46.48 Å / SU ML: 0.2857 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1387
RfactorNum. reflection% reflection
Rfree0.2425 1506 5.08 %
Rwork0.1876 --
obs0.1904 29641 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 9 339 3029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072736
X-RAY DIFFRACTIONf_angle_d0.8063691
X-RAY DIFFRACTIONf_chiral_restr0.0521408
X-RAY DIFFRACTIONf_plane_restr0.0053487
X-RAY DIFFRACTIONf_dihedral_angle_d28.9471033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.910.37691320.34172469X-RAY DIFFRACTION96.69
1.91-1.980.32681390.30042494X-RAY DIFFRACTION97.77
1.98-2.060.32411450.26142485X-RAY DIFFRACTION97.55
2.06-2.150.27281250.22582540X-RAY DIFFRACTION98.3
2.15-2.260.28511400.20612517X-RAY DIFFRACTION98.88
2.26-2.410.2741250.20262584X-RAY DIFFRACTION99.6
2.41-2.590.25961520.19632553X-RAY DIFFRACTION99.82
2.59-2.850.30681280.1992605X-RAY DIFFRACTION99.74
2.85-3.270.24781210.18282615X-RAY DIFFRACTION99.74
3.27-4.110.20691530.14192616X-RAY DIFFRACTION99.6
4.11-46.50.1681460.1422657X-RAY DIFFRACTION95.99

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